How to Know If You Have a Gut Microbiome Imbalance

Restoring the balance of your gut microbiome can be an ongoing battle. An imbalanced gut, where bad bacteria run the show, can lead to skin issues (e.g. Rosacea, Eczema), autoimmune diseases, and allergies. Poor gut health is also linked to endocrine disorders, endometriosis, candida, and everyone’s favourite the incurably irritable, IBS.

Blue gut microbiome bacteria against a black background

The gut is home to trillions of microorganisms that play a crucial role in our overall health. If you want to meet a few of them and find out what they’re eating you can do that here. Otherwise, let’s dive into the main triggers of bad bacteria overgrowth, the stressors that can worsen it and a few ways to restore balance. So. What causes the bad bacteria in the gut to go rogue? 

What upsets gut bacteria balance?

Now, obviously, you don’t need me to tell you, If have gut issues, you should speak to a healthcare professional. Now we’ve got that out of the way, here are a few of the biggest culprits:


Most antibiotics kill both good and bad bacteria in the gut. Eating more soluble fibre reduces antibiotic-resistant microbes, but taking probiotics and an antibiotic chaser isn’t going to help your gut microbiome.

A recent study also showed that antibiotics can weaken the immune system, and make room for fungal infections like Candida.

Just to be clear: I am in no way suggesting that you not take your prescribed antibiotics. When they’re needed, they’re needed.

I know you know this, like I know you know not to take health advice from an actor on the internet. To illustrate my point, Grammarly just informed me that I spelt internet wrong.

I digress.

Do yourself a favour and load up on the probiotics after you finish the course. 

Again actor/writer, not MD.

I could probably also sing you a song about it but I’m pretty sure nobody’s asking for Gut Health: The Musical.


Diet and poor gut health

A diet that’s high in processed foods, refined carbohydrates, unhealthy fats and sugar can negatively impact gut bacteria. Such a diet means bad bacteria thrive while good bacteria struggle, leading to an imbalanced gut microbiome.

Variety of gut diverse healthy foods.

In The Way We Eat Now, food writer and historian, Bee Wilson (got to love someone who studies old food) explains how our gut microbiome is less diverse than before.

Human beings only began farming around 10,000 years ago. Up until very recently, we lived in the communities we were born in and ate the food around us. In only the last 100 years, we’ve seen industrialisation, mass production and a global standard diet.

We have access to food from all over the world at the click of a button, anytime, day or night- sometimes free if it takes longer than 30 minutes to arrive.

Wilson argues that food is abundant in the West. Sugars, fats and high-carb grains were only occasional indulgences before the last 50 years or so. Now they’re available whenever we want them. She points out that at no other time in history have we had access to the sheer quantity of food available to us in the West.

And that’s not necessarily a good thing. 

We are full yet undernourished. We eat fast food on the go, between meetings and work 40 hours plus a week.

No wonder our gut microbiome is wondering what the actual frack has happened. 

Beige carbs, beige microbiome

Crisps in a bowl

A diet filled with beige carbs like white bread, pasta, and rice, has led to a decrease in the consumption of fibre-rich foods. Foods high in fat, carbs, and sugar are also often stripped of fibre and essential nutrients; crucial for maintaining a healthy gut.

Lack of fibre has also been linked to several gut-related problems. I think you know what I’m going to say. I can’t find any research that hasn’t said something along the lines of, “Put the chip down, have a carrot”.


Back away from the chips. Have the fibrous fruit or vegetable of your choice.

Added sugar is not your friend

Despite what the fad diets prescribe, you can’t eliminate sugar entirely and it would be stupid to try. Sugar is a type of carbohydrate that is found naturally in fruits, vegetables, and dairy products. We need this kind of sugar. The body breaks this sugar down into glucose and turns it into energy.

The problem is that along with natural sugars, we also have the refined kind.

Multicoloured glazed donuts in a pile.

This is added to processed foods, such as sweets, cakes, and basically everything that tastes nice and most of the gluten-free aisle. Without it, most prepackaged gluten-free food would taste like cardboard. This is largely a tolerance thing; the more we get used to a certain level of sweetness, the more we need. Sugar is added to gluten-free bread simply because it tastes better.  Or it tastes of something anyway.

High sugar is hard to avoid, despite the recent crackdowns on multi-buys and buy 1 get 1 free promotions. Most restrictions seem to cover where shops can display products rather than the quantities of high fat, sugar and salt.

Here’s a study that shows high sugar can “stagger the balance” of your gut. Even artificial sweeteners take their toll.

So cooking from scratch it is, then.

Lack of sleep and poor gut health

Hand holding a lit phone screen in the dark.

Here’s a question. Do the Gen Z’s know what the tube in YouTube means? Do any of us? I feel old. I probably look it too as I tend to be awake at 3 a.m. doom scrolling, lost down the Youtube rabbit hole or with a book I can’t put down.  Yes, I know that isn’t healthy. We also know from Matthew Walker’s very scary book, lack of sleep will age you, cause dementia and other Bad Things. It’s a good read; though it did keep me up very late.

Sleep is crucial for the body to repair and regenerate. Chronic lack of sleep can also harm gut bacteria, which as we know leads to an imbalanced gut microbiome. Lack of sleep is also a big IBS trigger. This is unfortunate as getting a decent night’s sleep gets harder as you age. It seems to be an occupational hazard of adulting from your 40s onward. Sadly, not enough sleep causes inflammation which leads to a host of health issues like Autoimmune and Cardiovascular diseases.

Stress, poor sleep and high sugar.

Try and avoid the big 3 and you’ll improve the balance of good and bad bacteria in the gut. How do you avoid these things in modern life? Well, with difficulty. Maybe start by not reading this stuff right before bed. You’ll thank me for it when you don’t look like the Walking Dead tomorrow.

This is your gut microbiome on stress

Stress triggers the release of cortisol, a hormone that can negatively impact the gut microbiome.

As I’m writing this I notice my hunched position and pain in my back from where I’ve been leaning towards the laptop for the last hour. Tiredness is beginning to win and the to-do list isn’t actually any shorter.  

On any given day, we experience a variety of factors that can affect the flora in our gut. It’s no secret that stress, mental and physical is a component. Studies show that eating while reading something stressful, can cause imbalances in the gut microbiome. That quick email check or “lunch & learn” while you’re trying to get a sandwich down is probably not doing you any favours. Eating while walking or eating too fast can also count as physical stressors that can lead to inflammation and imbalances in the gut. 

Post-pandemic stress is gut stress

Yellow post-it on window reading -'Sorry we are closed-Covid-19'

During the worst months of the pandemic, routines came to an abrupt halt. We all began living a bizarro standstill existence, punctuated by government-endorsed walks that we may or may not have taken. Daily exercise was more likely to involve a visit to the biscuit tin without the awkward small talk of the office kitchen. Marvellous.

My own experience of working from home was a mixed bag, characterized by prolonged periods of sitting and eating copious amounts of chocolate. The stress that permeated those days didn’t help, pushing me further down the path of an imbalanced gut.

While nothing could have prepared us for the strange turn that life took in 2020, for some, it can never go back to how it was before. No matter how much hybrid working may be foisted upon us.

The New Normal is worse than the Old Normal

For those of us with gut health issues (around 10-20% of the UK population and at least 70 million people in the US), going back to the office is not simple.

According to the Association of UK Dieticians, nearly half of those with poor gut health were worried; 87% of employers are not understanding.  

At least the new normal is beginning to recognise that the pandemic is a worldwide “mass trauma”. It has taken a huge toll on mental health.

Isolation may have caused PTSD, depression and anxiety. But, being forced to return is having a similar effect on those who’ve realised their pre-pandemic work-life balance wasn’t good enough. 

There’s a lot we can’t change, but we can start by taking back control of gut health. Even one less trip to the biscuit tin can go a long way to improving mood and mental health. 

Improving gut health with prebiotics and probiotics


A good way to promote a healthy gut is by eating prebiotic foods. These are foods that contain fibre that gut bacteria can feed on. Prebiotic foods include whole grains, bananas, apples, cabbage, chickpeas, lentils, beans, onions and garlic.

Now, that list is a little depressing for us IBS sufferers as they’re all triggers. The key is moderation and a good dose of probiotics until you’re better able to tolerate some of these foods. If you’re struggling with IBS triggers you may want to try an elimination diet, but make sure it’s doctor-approved.


These are live bacteria and yeasts that are good for your health, specifically for your gut. They can be found in certain foods and supplements, and they work to balance the good and bad bacteria in your gut.

Probiotics have numerous benefits. They can reduce inflammation, boost the immune system, and improve nutrient absorption. When you introduce probiotics, they can help outnumber and even eliminate the bad bacteria, restoring balance to your gut microbiome. 

Here are some of the most effective probiotic supplements I’ve found:

You’ll know they’re working if you’re going more frequently and feeling less pain and bloating.

Probiotics are also said to improve sleep, mood, memory and focus. Also worth giving a try is Alpro’s Plain No Sugars probiotic yoghurt. It’s the best probiotic yoghurt I’ve found and it does wonders. 

Although it’s not clear how effective supplemental forms of probiotics are, based on my personal experience, they’ve helped. You may want to see if they could be helpful for you as well. If not stick with the yoghurts, kefir, kombucha and sourdough.  Get the right nutrition, and cut way back on the sugar instead.

And thanks to this gut health test kit from Holland and Barrett you can now test your microbiome at home. It offers a dietary fibre breakdown, probiotics and beneficial bacteria report and personalised suggestions to improve gut health and optimise vitamin synthesis.

So that’s it

By eating a diverse and balanced diet rich in probiotic and prebiotic foods, you can help support the balance of good bacteria in your gut. Also avoid processed sugar, alcohol, junk food, lack of sleep, and stress. Considering our modern lives it’s amazing poor gut health stats aren’t much higher than they are. But by taking care of your gut, you’ll not only feel better physically but also reap the mental health benefits. 

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